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Fig. 3 | BMC Bioinformatics

Fig. 3

From: New tools to analyze overlapping coding regions

Fig. 3

a Output from the program FRESCo [18], when run on the Gag reading frame of an alignment of 200 sequences from the LANL HIV-1 database using 50 nt windows. Note the precipitous drop in dN/dS value at the beginning of Gag-Pol overlap region. b Values of d N/d S, branch length, and transition/transversion rate (see [8] for definitions) for the 52 nt Gag-Pol overlap regions within a multiple alignment from Rfam family RF00480 as well as from 52 nt RNA sequences generated by the programs RNAsampleCDS and RNAiFold. These programs generate sequences that code peptides, each of whose amino acids has BLOSUM62 similarity of either 0 or 1 to the corresponding amino acids in the Gag [resp. Pol] reading frame of the peptide translated by the 52 nt HIV-1 overlap region of [2] or by GenBank accession code AF033819.3/1631-1681. The program RNAsampleCDS ensures only coding requirements, while RNAiFold ensures both coding requirements and that the 52 nt RNAs fold into the minimum free energy structure of the Gag-Pol overlap region of HIV-1 from [2] and GenBank accession code AF033819.3/1631-1682

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